What Constitutes Messages in Junction Tree Algorithm?
I think an example could make you understand better.
Suppose you want to calculate $P(X|S)$, you now need to put evidence on $S$(so you have to change all tables where $S$ appears making probability zero where $S$ does not appear).
At this point, you can proceed with the collect and distribute method in order to propagate the evidence throughout the graph, in order to maintain the global consistency property. Now you can choose any $cluster\space V$ that contains $X$, marginalize with respect to $S$, and the job is done.